Update VQSR commands to follow recent GATK best practices

[tnyamaguchi]

It looks like they have updated the VQSR models.

https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering

Also, for WXS samples, we may want to remove the DP from the model as suggested here.
https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR-